org.molgenis.omx.observ.target

Class Ontology

java.lang.Object

org.molgenis.data.support.AbstractEntity

org.molgenis.omx.observ.target.Ontology

All Implemented Interfaces:

Serializable, Entity, Autoid, Identifiable

@Entity
public class Ontology
extends AbstractEntity
implements Entity, Identifiable

Ontology: Ontology defines a reference to an ontology or controlled vocabulary from which well-defined and stable (ontology) terms can be obtained. Each Ontology should have a unique identifer, for instance: Gene Ontology, Mammalian Phenotype, Human Phenotype Ontology, Unified Medical Language System, Medical Subject Headings, etc. Also a abbreviation is required, for instance: GO, MP, HPO, UMLS, MeSH, etc. Use of existing ontologies/vocabularies is recommended to harmonize phenotypic feature and value descriptions. But one can also create a 'local' Ontology. The Ontology class maps to FuGE::Ontology, MAGE-TAB::TermSourceREF. .

Author:

MOLGENIS generator

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	ENTITY_NAME
static String	ID
static String	IDENTIFIER
static String	NAME
static String	ONTOLOGYACCESSION
static String	ONTOLOGYURI

Constructor Summary

Constructors

Constructor and Description
Ontology()

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(Object obj)
Object	get(String name) Generic getter.
Iterable<String>	getAttributeNames()
EntityMetaData	getEntityMetaData()
String	getEntityName()
Integer	getId() Get the automatically generated internal id, only for internal use..
String	getIdentifier() Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
Integer	getIdValue()
List<String>	getLabelAttributeNames()
String	getName() Get the human readible name, not necessary unique..
String	getOntologyAccession() Get the A accession that uniquely identifies the ontology (typically an acronym).
String	getOntologyURI() Get the (Optional) A URI that references the location of the ontology..
int	hashCode()
void	set(Entity entity, boolean strict)
void	set(String attributeName, Object value)
void	setId(Integer id) Set the automatically generated internal id, only for internal use..
void	setIdentifier(String identifier) Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g.
void	setName(String name) Set the human readible name, not necessary unique..
void	setOntologyAccession(String ontologyAccession) Set the A accession that uniquely identifies the ontology (typically an acronym).
void	setOntologyURI(String ontologyURI) Set the (Optional) A URI that references the location of the ontology..
String	toString()
String	toString(boolean verbose)

Methods inherited from class org.molgenis.data.support.AbstractEntity

getBoolean, getDate, getDouble, getEntities, getEntity, getInt, getIntList, getLabelValue, getList, getLong, getString, getTimestamp, getUtilDate, isObjectRepresentation, set, setValuesFromString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.molgenis.data.Entity

getBoolean, getDate, getDouble, getEntities, getEntity, getInt, getIntList, getLabelValue, getList, getLong, getString, getTimestamp, getUtilDate, set

Field Detail

ENTITY_NAME

public static final String ENTITY_NAME

See Also:

Constant Field Values

ID

public static final String ID

See Also:

Constant Field Values

IDENTIFIER

public static final String IDENTIFIER

See Also:

Constant Field Values

NAME

public static final String NAME

See Also:

Constant Field Values

ONTOLOGYACCESSION

public static final String ONTOLOGYACCESSION

See Also:

Constant Field Values

ONTOLOGYURI

public static final String ONTOLOGYURI

See Also:

Constant Field Values

Constructor Detail

Ontology

public Ontology()

Method Detail

getEntityName

public String getEntityName()

getId

public Integer getId()

Get the automatically generated internal id, only for internal use..

Specified by:

getId in interface Autoid

Returns:

id.

setId

public void setId(Integer id)

Set the automatically generated internal id, only for internal use..

Specified by:

setId in interface Autoid

Parameters:

id -

getIdentifier

public String getIdentifier()

Get the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234.

Specified by:

getIdentifier in interface Identifiable

Returns:

identifier.

setIdentifier

public void setIdentifier(String identifier)

Set the user supplied or automatically assigned (using a decorator) unique and short identifier, e.g. MA1234.

Specified by:

setIdentifier in interface Identifiable

Parameters:

identifier -

getName

public String getName()

Get the human readible name, not necessary unique..

Specified by:

getName in interface Identifiable

Returns:

name.

setName

public void setName(String name)

Set the human readible name, not necessary unique..

Specified by:

setName in interface Identifiable

Parameters:

name -

getOntologyAccession

public String getOntologyAccession()

Get the A accession that uniquely identifies the ontology (typically an acronym). E.g. GO, MeSH, HPO..

Returns:

ontologyAccession.

setOntologyAccession

public void setOntologyAccession(String ontologyAccession)

Set the A accession that uniquely identifies the ontology (typically an acronym). E.g. GO, MeSH, HPO..

Parameters:

ontologyAccession -

getOntologyURI

public String getOntologyURI()

Get the (Optional) A URI that references the location of the ontology..

Returns:

ontologyURI.

setOntologyURI

public void setOntologyURI(String ontologyURI)

Set the (Optional) A URI that references the location of the ontology..

Parameters:

ontologyURI -

get

public Object get(String name)

Generic getter. Get the property by using the name.

Specified by:

get in interface Entity

set

public void set(Entity entity,
       boolean strict)

Specified by:

set in interface Entity

toString

public String toString()

Overrides:

toString in class AbstractEntity

toString

public String toString(boolean verbose)

getIdValue

public Integer getIdValue()

Specified by:

getIdValue in interface Entity

getAttributeNames

public Iterable<String> getAttributeNames()

Specified by:

getAttributeNames in interface Entity

getLabelAttributeNames

public List<String> getLabelAttributeNames()

Specified by:

getLabelAttributeNames in interface Entity

set

public void set(String attributeName,
       Object value)

Specified by:

set in interface Entity

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getEntityMetaData

public EntityMetaData getEntityMetaData()

Specified by:

getEntityMetaData in interface Entity